9rhm

Phospho-MCM double hexamer bound to Sld3-Sld7-Cdc45 on ARS1 DNA

Method: ELECTRON MICROSCOPY Dmax: 258.3 Å Quality: EXCELLENT

1. Protein Identity and Related Structures Protein Identity & Related Structures

Mitochondrial morphogenesis protein SLD7

Saccharomyces cerevisiae

UniProt Q08457

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 17 DNA 2 PDB declaration: 19-meric(19) Consistent with all polymer counts Chain A; UniProt 1–257 Chain R; UniProt 1–257 Not recorded DNA replication regulator SLD3 × 2 (P53135) DNA (53-MER) × 1 DNA (53-MER) × 1 Cell division control protein 45 × 1 (Q08032) DNA replication licensing factor MCM2 × 2 (P29469) DNA replication licensing factor MCM3 × 2 (P24279) DNA replication licensing factor MCM4 × 2 (P30665) Minichromosome maintenance protein 5 × 2 (P29496) DNA replication licensing factor MCM6 × 2 (P53091) DNA replication licensing factor MCM7 × 2 (P38132) ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SLD7_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–257; UniProt 1–257 Author chain R; PDBConstruct 1–257; UniProt 1–257

DNA replication regulator SLD3

Saccharomyces cerevisiae

UniProt P53135

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 17 DNA 2 PDB declaration: 19-meric(19) Consistent with all polymer counts Chain H; UniProt 1–668 Chain I; UniProt 1–668 Not recorded Mitochondrial morphogenesis protein SLD7 × 2 (Q08457) DNA (53-MER) × 1 DNA (53-MER) × 1 Cell division control protein 45 × 1 (Q08032) DNA replication licensing factor MCM2 × 2 (P29469) DNA replication licensing factor MCM3 × 2 (P24279) DNA replication licensing factor MCM4 × 2 (P30665) Minichromosome maintenance protein 5 × 2 (P29496) DNA replication licensing factor MCM6 × 2 (P53091) DNA replication licensing factor MCM7 × 2 (P38132) ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SLD3_YEAST
Isoform
PDB entities 2
Chains and sequence ranges Author chain H; PDBConstruct 1–668; UniProt 1–668 Author chain I; PDBConstruct 1–668; UniProt 1–668

Cell division control protein 45

Saccharomyces cerevisiae

UniProt Q08032

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 17 DNA 2 PDB declaration: 19-meric(19) Consistent with all polymer counts Chain E; UniProt 1–197 Chain E; UniProt 204–650 Not recorded Mitochondrial morphogenesis protein SLD7 × 2 (Q08457) DNA replication regulator SLD3 × 2 (P53135) DNA (53-MER) × 1 DNA (53-MER) × 1 DNA replication licensing factor MCM2 × 2 (P29469) DNA replication licensing factor MCM3 × 2 (P24279) DNA replication licensing factor MCM4 × 2 (P30665) Minichromosome maintenance protein 5 × 2 (P29496) DNA replication licensing factor MCM6 × 2 (P53091) DNA replication licensing factor MCM7 × 2 (P38132) ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

34 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CDC45_YEAST
Isoform
PDB entities 5
Chains and sequence ranges Author chain E; PDBConstruct 1–197; UniProt 1–197 Author chain E; PDBConstruct 211–657; UniProt 204–650

DNA replication licensing factor MCM2

Saccharomyces cerevisiae

UniProt P29469

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 17 DNA 2 PDB declaration: 19-meric(19) Consistent with all polymer counts Chain 2; UniProt 1–868 Chain a; UniProt 1–868 Not recorded Mitochondrial morphogenesis protein SLD7 × 2 (Q08457) DNA replication regulator SLD3 × 2 (P53135) DNA (53-MER) × 1 DNA (53-MER) × 1 Cell division control protein 45 × 1 (Q08032) DNA replication licensing factor MCM3 × 2 (P24279) DNA replication licensing factor MCM4 × 2 (P30665) Minichromosome maintenance protein 5 × 2 (P29496) DNA replication licensing factor MCM6 × 2 (P53091) DNA replication licensing factor MCM7 × 2 (P38132) ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

51 other PDB entries and 51 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MCM2_YEAST
Isoform
PDB entities 6
Chains and sequence ranges Author chain 2; PDBConstruct 1–868; UniProt 1–868 Author chain a; PDBConstruct 1–868; UniProt 1–868

DNA replication licensing factor MCM3

Saccharomyces cerevisiae

UniProt P24279

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 17 DNA 2 PDB declaration: 19-meric(19) Consistent with all polymer counts Chain 3; UniProt 1–971 Chain b; UniProt 1–971 Not recorded Mitochondrial morphogenesis protein SLD7 × 2 (Q08457) DNA replication regulator SLD3 × 2 (P53135) DNA (53-MER) × 1 DNA (53-MER) × 1 Cell division control protein 45 × 1 (Q08032) DNA replication licensing factor MCM2 × 2 (P29469) DNA replication licensing factor MCM4 × 2 (P30665) Minichromosome maintenance protein 5 × 2 (P29496) DNA replication licensing factor MCM6 × 2 (P53091) DNA replication licensing factor MCM7 × 2 (P38132) ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

59 other PDB entries and 59 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MCM3_YEAST
Isoform
PDB entities 7
Chains and sequence ranges Author chain 3; PDBConstruct 36–1006; UniProt 1–971 Author chain b; PDBConstruct 36–1006; UniProt 1–971

DNA replication licensing factor MCM4

Saccharomyces cerevisiae

UniProt P30665

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 17 DNA 2 PDB declaration: 19-meric(19) Consistent with all polymer counts Chain 4; UniProt 1–933 Chain c; UniProt 1–933 Not recorded Mitochondrial morphogenesis protein SLD7 × 2 (Q08457) DNA replication regulator SLD3 × 2 (P53135) DNA (53-MER) × 1 DNA (53-MER) × 1 Cell division control protein 45 × 1 (Q08032) DNA replication licensing factor MCM2 × 2 (P29469) DNA replication licensing factor MCM3 × 2 (P24279) Minichromosome maintenance protein 5 × 2 (P29496) DNA replication licensing factor MCM6 × 2 (P53091) DNA replication licensing factor MCM7 × 2 (P38132) ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

58 other PDB entries and 58 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MCM4_YEAST
Isoform
PDB entities 8
Chains and sequence ranges Author chain 4; PDBConstruct 1–933; UniProt 1–933 Author chain c; PDBConstruct 1–933; UniProt 1–933

Minichromosome maintenance protein 5

Saccharomyces cerevisiae

UniProt P29496

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 17 DNA 2 PDB declaration: 19-meric(19) Consistent with all polymer counts Chain 5; UniProt 1–775 Chain d; UniProt 1–775 Not recorded Mitochondrial morphogenesis protein SLD7 × 2 (Q08457) DNA replication regulator SLD3 × 2 (P53135) DNA (53-MER) × 1 DNA (53-MER) × 1 Cell division control protein 45 × 1 (Q08032) DNA replication licensing factor MCM2 × 2 (P29469) DNA replication licensing factor MCM3 × 2 (P24279) DNA replication licensing factor MCM4 × 2 (P30665) DNA replication licensing factor MCM6 × 2 (P53091) DNA replication licensing factor MCM7 × 2 (P38132) ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

54 other PDB entries and 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MCM5_YEAST
Isoform
PDB entities 9
Chains and sequence ranges Author chain 5; PDBConstruct 1–775; UniProt 1–775 Author chain d; PDBConstruct 1–775; UniProt 1–775

DNA replication licensing factor MCM6

Saccharomyces cerevisiae

UniProt P53091

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 17 DNA 2 PDB declaration: 19-meric(19) Consistent with all polymer counts Chain 6; UniProt 1–1017 Chain e; UniProt 1–1017 Not recorded Mitochondrial morphogenesis protein SLD7 × 2 (Q08457) DNA replication regulator SLD3 × 2 (P53135) DNA (53-MER) × 1 DNA (53-MER) × 1 Cell division control protein 45 × 1 (Q08032) DNA replication licensing factor MCM2 × 2 (P29469) DNA replication licensing factor MCM3 × 2 (P24279) DNA replication licensing factor MCM4 × 2 (P30665) Minichromosome maintenance protein 5 × 2 (P29496) DNA replication licensing factor MCM7 × 2 (P38132) ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

58 other PDB entries and 58 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MCM6_YEAST
Isoform
PDB entities 10
Chains and sequence ranges Author chain 6; PDBConstruct 1–1017; UniProt 1–1017 Author chain e; PDBConstruct 1–1017; UniProt 1–1017

DNA replication licensing factor MCM7

Saccharomyces cerevisiae

UniProt P38132

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 17 DNA 2 PDB declaration: 19-meric(19) Consistent with all polymer counts Chain 7; UniProt 1–845 Chain f; UniProt 1–845 Not recorded Mitochondrial morphogenesis protein SLD7 × 2 (Q08457) DNA replication regulator SLD3 × 2 (P53135) DNA (53-MER) × 1 DNA (53-MER) × 1 Cell division control protein 45 × 1 (Q08032) DNA replication licensing factor MCM2 × 2 (P29469) DNA replication licensing factor MCM3 × 2 (P24279) DNA replication licensing factor MCM4 × 2 (P30665) Minichromosome maintenance protein 5 × 2 (P29496) DNA replication licensing factor MCM6 × 2 (P53091) ZN ZINC ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

55 other PDB entries and 55 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MCM7_YEAST
Isoform
PDB entities 11
Chains and sequence ranges Author chain 7; PDBConstruct 1–845; UniProt 1–845 Author chain f; PDBConstruct 1–845; UniProt 1–845

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9rhm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9rhm
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id9rhm
Deposition date deposition_date2025-06-09
Structure title titlePhospho-MCM double hexamer bound to Sld3-Sld7-Cdc45 on ARS1 DNA
Keywords keywordsMacromolecular Complex, DNA, ATPase, Helicase, MCM2-7, REPLICATION; REPLICATION
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier71.74
Radius of gyration Rg (electron density) rg_electron72.00
Forward intensity I(0) i013975700000.00
Molecular weight molecular_weight980310.0 kDa
Excluded volume excluded_volume1218500 ų
Envelope volume envelope_volume1947500 ų
Hydration-shell volume shell_volume216580 ų
Envelope diameter envelope_diameter223.4
Shell Rg shell_rg77.25
Envelope Rg envelope_rg70.17
Shape Rg shape_rg72.03
Total Rg total_rg71.98
Total atoms total_atoms68681
Residues n_residues8507
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax258.3
Rg (real space) rg_real74.84
Rg uncertainty (real space) rg_real_error1.34
I(0) (real space) i0_real1.3980e+10
I(0) uncertainty (real space) i0_real_error2.7350e+08
Rg (reciprocal space) rg_reciprocal71.94
I(0) (reciprocal space) i0_reciprocal13980000000.0000
Solution quality estimate total_estimate0.9009
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary82.2
Skewness Skewness skewness0.487
Kurtosis Kurtosis kurtosis-0.079
Angular range angular_range— – 0.1100 −1
Current regularization parameter α current_alpha1.1110
Highest regularization parameter α highest_alpha4763000000.0000
Real-space data points n_real_points23
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.761; Stabil: 0.878; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.852

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (14)

8. Citations (1)

9. Files and Curves (10)